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Human sepiapterin reductase in complex with the cofactor NADP+ and the trypthophan metabolite xanthurenic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HWK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 2% W/V PEG1000, 1.9 M Ammonium sulfate, 0.1 M Hepes pH7.5
Crystal Properties Matthews coefficient Solvent content 4.89 74.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.964 α = 90 b = 143.964 β = 90 c = 180.74 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2014-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.35 124.676 100 0.106 0.111 0.031 20 12.9 88165 88165 57.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.48 100 1.085 1.085 0.307 0.7 13.3 12862
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4HWK 2.35 124.676 83471 4633 99.99 0.1825 0.1808 0.2139 RANDOM 50.093
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.83 0.41 0.83 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.316 r_dihedral_angle_4_deg 20.15 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 6.388 r_mcangle_it 6.24 r_mcbond_it 4.453 r_mcbond_other 4.451 r_angle_refined_deg 1.446 r_angle_other_deg 0.732 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.316 r_dihedral_angle_4_deg 20.15 r_dihedral_angle_3_deg 13.857 r_dihedral_angle_1_deg 6.388 r_mcangle_it 6.24 r_mcbond_it 4.453 r_mcbond_other 4.451 r_angle_refined_deg 1.446 r_angle_other_deg 0.732 r_chiral_restr 0.085 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7744 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 286
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction